Chlorine in PDB 6nj1: Crystal Structure of Class A Beta-Lactamase From Clostridium Kluyveri Dsm 555

Enzymatic activity of Crystal Structure of Class A Beta-Lactamase From Clostridium Kluyveri Dsm 555

All present enzymatic activity of Crystal Structure of Class A Beta-Lactamase From Clostridium Kluyveri Dsm 555:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Class A Beta-Lactamase From Clostridium Kluyveri Dsm 555, PDB code: 6nj1 was solved by K.Michalska, L.Welk, M.Endres, A.Joachimiak, Center For Structuralgenomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.20 / 1.40
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 66.878, 66.878, 119.795, 90.00, 90.00, 120.00
R / Rfree (%) 12.4 / 15.1

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Class A Beta-Lactamase From Clostridium Kluyveri Dsm 555 (pdb code 6nj1). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Class A Beta-Lactamase From Clostridium Kluyveri Dsm 555, PDB code: 6nj1:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 6nj1

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Chlorine binding site 1 out of 5 in the Crystal Structure of Class A Beta-Lactamase From Clostridium Kluyveri Dsm 555


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Class A Beta-Lactamase From Clostridium Kluyveri Dsm 555 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:35.5
occ:1.00
 H A:ALA121 2.4 28.7 1.0
HZ3 A:LYS125 2.5 59.1 1.0
HA A:PRO122 3.1 30.5 1.0
HD3 A:LYS125 3.1 43.0 1.0
HA A:TYR120 3.2 30.9 1.0
N A:ALA121 3.3 23.9 1.0
O A:HOH589 3.3 38.2 1.0
NZ A:LYS125 3.4 49.3 1.0
O A:SER119 3.5 28.3 0.5
HD3 A:PRO122 3.5 31.1 1.0
N A:PRO122 3.6 24.3 1.0
HZ2 A:LYS125 3.6 59.1 1.0
C A:ALA121 3.6 23.4 1.0
CA A:PRO122 3.7 25.4 1.0
HB3 A:PRO122 3.8 31.2 1.0
O A:SER119 3.8 29.8 0.5
HD1 A:TYR120 3.9 32.8 1.0
HZ1 A:LYS125 3.9 59.1 1.0
CD A:LYS125 4.0 35.8 1.0
O A:ALA121 4.0 24.7 1.0
CA A:TYR120 4.0 25.8 1.0
CD A:PRO122 4.0 25.9 1.0
CA A:ALA121 4.1 24.0 1.0
C A:TYR120 4.1 24.2 1.0
CE A:LYS125 4.1 42.7 1.0
CB A:PRO122 4.3 26.0 1.0
HE2 A:LYS125 4.3 51.2 1.0
CD1 A:TYR120 4.3 27.3 1.0
O A:HOH519 4.3 55.4 1.0
HD2 A:LYS125 4.4 43.0 1.0
C A:SER119 4.5 27.6 0.5
HB3 A:ALA121 4.5 30.6 1.0
C A:SER119 4.6 27.9 0.5
N A:TYR120 4.7 25.1 1.0
HB3 A:LYS125 4.8 37.0 1.0
HD2 A:PRO122 4.8 31.1 1.0
CG A:PRO122 4.8 24.9 1.0
HA A:ALA121 4.8 28.9 1.0
CE1 A:TYR120 4.8 28.9 1.0
HE1 A:TYR120 4.8 34.7 1.0
CB A:ALA121 4.9 25.5 1.0
CG A:TYR120 4.9 25.8 1.0
HG2 A:LYS125 5.0 39.1 1.0

Chlorine binding site 2 out of 5 in 6nj1

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Chlorine binding site 2 out of 5 in the Crystal Structure of Class A Beta-Lactamase From Clostridium Kluyveri Dsm 555


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Class A Beta-Lactamase From Clostridium Kluyveri Dsm 555 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:28.7
occ:0.50
 H A:LEU109 2.5 28.0 1.0
HG3 A:GLN108 3.0 28.0 1.0
HA A:GLN108 3.0 26.8 1.0
O A:HOH634 3.3 33.0 1.0
N A:LEU109 3.3 23.4 1.0
HB3 A:LEU109 3.6 33.6 1.0
HB2 A:LEU109 3.7 33.6 1.0
CG A:GLN108 3.9 23.3 1.0
CA A:GLN108 3.9 22.3 1.0
CB A:LEU109 4.0 28.0 1.0
HG2 A:GLN108 4.0 28.0 1.0
C A:GLN108 4.1 21.4 1.0
CA A:LEU109 4.2 23.6 1.0
CB A:GLN108 4.4 22.2 1.0
HE21 A:GLN108 4.4 28.2 1.0
O A:LEU109 4.5 29.9 1.0
O A:LYS107 4.6 26.6 1.0
HB2 A:GLN108 4.6 26.7 1.0
C A:LEU109 4.9 25.8 1.0
CD A:GLN108 4.9 21.6 1.0
N A:GLN108 5.0 21.6 1.0
NE2 A:GLN108 5.0 23.5 1.0

Chlorine binding site 3 out of 5 in 6nj1

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Chlorine binding site 3 out of 5 in the Crystal Structure of Class A Beta-Lactamase From Clostridium Kluyveri Dsm 555


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Class A Beta-Lactamase From Clostridium Kluyveri Dsm 555 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:27.2
occ:0.90
 HG A:SER139 2.3 26.0 1.0
HA A:ALA140 3.0 21.2 1.0
HE2 A:PHE144 3.0 32.8 1.0
O A:HOH579 3.0 26.7 1.0
OG A:SER139 3.1 21.6 1.0
O A:HOH713 3.1 47.7 1.0
HD2 A:PHE144 3.2 28.5 1.0
HD2 A:ARG143 3.2 22.0 1.0
O A:HOH691 3.4 41.1 1.0
HB3 A:SER139 3.5 23.7 1.0
HG13 A:ILE123 3.5 31.8 1.0
N A:ALA140 3.6 17.5 1.0
HB2 A:ARG143 3.6 21.4 1.0
CA A:ALA140 3.6 17.6 1.0
CE2 A:PHE144 3.7 27.3 1.0
C A:SER139 3.7 17.6 1.0
HB2 A:ALA140 3.7 23.3 1.0
CD2 A:PHE144 3.8 23.7 1.0
CB A:SER139 3.8 19.8 1.0
O A:SER139 3.8 18.4 1.0
H A:ALA140 3.9 21.0 1.0
CD A:ARG143 4.1 18.4 1.0
O A:HOH686 4.2 35.3 1.0
CB A:ALA140 4.2 19.4 1.0
O A:HOH672 4.2 42.1 1.0
HG21 A:ILE123 4.2 31.6 1.0
HG3 A:ARG143 4.3 21.7 1.0
CA A:SER139 4.4 18.3 1.0
CB A:ARG143 4.4 17.9 1.0
HE A:ARG143 4.4 22.8 1.0
CG1 A:ILE123 4.4 26.5 1.0
HD11 A:ILE123 4.5 34.9 1.0
HD12 A:ILE123 4.5 34.9 1.0
CG A:ARG143 4.5 18.1 1.0
HB3 A:ARG143 4.6 21.4 1.0
HB2 A:SER139 4.6 23.7 1.0
HB1 A:ALA140 4.6 23.3 1.0
CD1 A:ILE123 4.7 29.1 1.0
HD3 A:ARG143 4.7 22.0 1.0
NE A:ARG143 4.8 18.9 1.0
O A:GLU136 4.8 18.9 1.0
HA A:SER139 4.9 22.0 1.0
C A:ALA140 4.9 17.1 1.0
CZ A:PHE144 4.9 29.1 1.0
HG12 A:ILE123 5.0 31.8 1.0

Chlorine binding site 4 out of 5 in 6nj1

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Chlorine binding site 4 out of 5 in the Crystal Structure of Class A Beta-Lactamase From Clostridium Kluyveri Dsm 555


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Class A Beta-Lactamase From Clostridium Kluyveri Dsm 555 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:40.4
occ:1.00
 HZ2 A:LYS218 2.7 31.9 1.0
HG23 A:THR215 2.8 40.1 1.0
H A:THR215 2.8 32.7 1.0
HD2 A:LYS218 2.8 28.7 1.0
HA A:LEU214 2.9 30.4 1.0
NZ A:LYS218 3.4 26.6 1.0
HZ3 A:LYS218 3.5 31.9 1.0
N A:THR215 3.5 27.2 1.0
CD A:LYS218 3.6 23.9 1.0
O A:ILE213 3.7 29.8 1.0
CG2 A:THR215 3.7 33.4 1.0
HA A:LYS99 3.7 24.8 1.0
HD2 A:LYS99 3.7 39.1 1.0
HD3 A:LYS218 3.7 28.7 1.0
CA A:LEU214 3.8 25.4 1.0
HD22 A:LEU214 3.8 30.0 1.0
HD23 A:LEU214 3.8 30.0 1.0
HG22 A:THR215 4.0 40.1 1.0
CE A:LYS218 4.0 26.0 1.0
HZ1 A:LYS218 4.1 31.9 1.0
C A:LEU214 4.1 26.8 1.0
HD3 A:LYS99 4.2 39.1 1.0
HZ2 A:LYS99 4.2 46.4 1.0
HG21 A:THR215 4.2 40.1 1.0
HE3 A:LYS218 4.2 31.2 1.0
CD2 A:LEU214 4.3 25.0 1.0
HZ3 A:LYS99 4.4 46.4 1.0
CD A:LYS99 4.4 32.6 1.0
O A:LEU98 4.5 21.6 1.0
HB3 A:LEU214 4.5 29.7 1.0
CB A:THR215 4.5 31.7 1.0
OG1 A:THR215 4.6 30.1 1.0
C A:ILE213 4.6 29.2 1.0
CA A:THR215 4.6 27.4 1.0
HB2 A:LYS218 4.6 24.6 1.0
NZ A:LYS99 4.7 38.7 1.0
N A:LEU214 4.7 27.9 1.0
CA A:LYS99 4.7 20.6 1.0
CB A:LEU214 4.7 24.8 1.0
O A:LYS99 4.8 23.7 1.0
O A:HOH614 4.9 55.5 1.0
HG1 A:THR215 4.9 36.1 1.0
CG A:LYS218 4.9 22.4 1.0
HE2 A:LYS218 4.9 31.2 1.0
HA A:THR215 5.0 32.9 1.0

Chlorine binding site 5 out of 5 in 6nj1

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Chlorine binding site 5 out of 5 in the Crystal Structure of Class A Beta-Lactamase From Clostridium Kluyveri Dsm 555


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Class A Beta-Lactamase From Clostridium Kluyveri Dsm 555 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:20.1
occ:1.00
 H A:VAL246 2.5 21.5 1.0
HE A:ARG237 2.5 24.5 1.0
HG3 A:ARG237 3.0 24.6 1.0
HB A:VAL246 3.2 22.5 1.0
O A:HOH630 3.2 25.5 1.0
HA A:ILE245 3.2 23.9 1.0
NE A:ARG237 3.3 20.4 1.0
N A:VAL246 3.3 17.9 1.0
HG23 A:VAL246 3.6 25.7 1.0
HD3 A:ARG237 3.6 24.9 1.0
CD A:ARG237 3.8 20.8 1.0
CG A:ARG237 3.8 20.5 1.0
HG23 A:ILE245 3.9 25.4 1.0
CB A:VAL246 3.9 18.7 1.0
HH21 A:ARG237 4.0 24.7 1.0
CA A:ILE245 4.1 19.9 1.0
O A:VAL246 4.1 19.5 1.0
O A:HOH568 4.1 20.4 1.0
CA A:VAL246 4.1 18.4 1.0
O A:TRP244 4.1 27.5 1.0
C A:ILE245 4.2 19.3 1.0
CG2 A:VAL246 4.2 21.4 1.0
CZ A:ARG237 4.3 19.5 1.0
HG2 A:ARG237 4.3 24.6 1.0
HD12 A:ILE245 4.4 28.9 1.0
NH2 A:ARG237 4.5 20.6 1.0
HB2 A:ARG237 4.5 24.7 1.0
C A:VAL246 4.6 18.3 1.0
HG21 A:VAL246 4.6 25.7 1.0
HD13 A:ILE245 4.6 28.9 1.0
CG2 A:ILE245 4.7 21.2 1.0
HD2 A:ARG237 4.7 24.9 1.0
CB A:ARG237 4.8 20.6 1.0
HG22 A:ILE245 4.8 25.4 1.0
HA A:ARG237 4.9 24.5 1.0
C A:TRP244 4.9 23.9 1.0
HA A:VAL246 5.0 22.1 1.0
CD1 A:ILE245 5.0 24.1 1.0
CB A:ILE245 5.0 19.7 1.0

Reference:

K.Michalska, L.Welk, M.Endres, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of Class A Beta-Lactamase From Clostridium Kluyveri Dsm 555 To Be Published.
Page generated: Sat Dec 12 13:24:04 2020

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